Editorial: Theme issue on the ecology of soil microorganisms

Inoculation of common bean seed with diversified bacterial synthetic communities can induce deep modifications of both seed and seedling microbiota, even in living potting soil.

While Peltoniemi et al. ( 2023 ) demonstrates the potentially positive effect of adding tree bark as a forestry by-product to soil to enhance its fungal communities and carbon content, Lori et al. ( 2023 ) show that organic farming including manure addition affects the micr obiome.Manur e addition, ho w e v er, needs to be considered with caution since it can increase the spread of antimicr obial r esistance genes (Sardar et al. 2023 ).What the future can be of wet grassland soils under global change is demonstrated by Edw ar ds et al. ( 2023): higher plant productivity under future conditions with warmer climate and higher nutrient load may lead up to the switch of these ecosystems from C accumulators to C sources.Grasslands that are already affected should be restoredincluding their microbiomes.Ho w ever, such transition may take more time than hoped (Barber et al. 2023 ).
For ests ar e another ecosystem that has r ecentl y r eceiv ed particular attention due to their ability to ca ptur e and stor e C but also due to their vulnerability to climate change effects (Baldrian et al. 2023 ).Recycling of nutrients in forests is driven by micr oor ganisms and the rate of this process and the participating microbes depend on litter type, likely reflecting chemical composition (Min et al. 2023 ).Current forest management largely relies, to minimize costs of operation, on total removal of trees-clearcutting.Its deleterious effect on symbiotic soil fungi was demonstrated.In their paper, Martinovi ć et al. ( 2022 ) show that bacteria are m uc h less affected by tree removal and may thus help to maintain ecosystem functioning on clearcuts.On the other hand, drought effects, especiall y pr olonged dr oughts ov er m ultiple years affect bacterial communities more profoundly than fungal communities (Jaeger et al. 2023 ).Last decade sees an increasing frequency of forest disturbances including insect infestations.Choma et al. ( 2023 ) show how surviving trees help to maintain the diversity of ectomycorrhizal root-symbiotic fungi and thus contribute to stand r egener ation.Deadwood r etention is one of the measures to maintain forest ecosystem diversity.In their paper, Bosch et al. ( 2023 ) show that this is due to the presence of se v er al taxa of fungi and bacteria e v en within small volumes of deadwood.In addition to deadwood, also tree phyllosphere exhibits high beta-diversity due to the strong host tree selection of leaf-associated microorganisms (Yang et al. 2023 ) and is worth further investigation.
From the perspective of global change, peatlands are perhaps e v en mor e important than for ests .T hey stor e mor e carbon but may be also important sources of greenhouse gasses (GHG).Their micr obiology is, unfortunatel y, onl y partl y understood.Weil et al. ( 2023 ) show that bacterial communities are vertically stratified e v en considering members of a single archaeal order.While there are concerns that GHG fluxes may increase from peatlands, this may not necessarily be the case since their production can be limited by the availability of terminal electron acceptors (Song et al. 2023 ).Also alpine treeline ecosystems belong to those under high impact of global c hange.Unfortunatel y, the ecosystem shift connected to tree colonization of higher altitudes may lead to C loss (Mora vco vá et al. 2023 ).
Interactions of microorganisms are often complex and range from symbiosis to antagonism.In the ectomycorrhizal system of eucalyptus with its ectomycorrhizal fungal partner Pisolithus microcarpus , C flow to fungal biomass seems to mostly reflect the demand of the fungal partner (Stuart et al. 2023 ).In another symbiotic system, Medina et al. ( 2023 ) show that social amoeba can rescue its bacterial host from interspecific competition.Viral shunts ar e e v ents wher e bacteria ar e l ysed after induction of the l ytic cycle of the virus.Heffner et al. ( 2023 ) show that antibiotic addition can trigger this e v ent and thus affect bacterial communities thr ough activ ating their viruses.
The paper of Kopecky et al. ( 2023 ) tries to extend our general understanding of environmental factors from microbiome composition to its function.They show that soil properties-pH and organic matter content-not only affect microbiome composition, but also its function-metabolic profiles of its individual members, soil actinomycetes in this particular case.
Ov er all, this thematic issue shows that microbial ecology has the potential to increase our understanding of future of microbiomes and help us to manage ecosystems in a more sustainable manner.Considering the r a pid c hanges of envir onmental conditions, these topics will r emain highl y important in the coming years.We are already looking forw ar d to the developments that will be presented at the 5th Ecology of Soil Micr oor ganisms conferences that will be held in Helsinki in 2025.

Petr Baldrian
Laboratory of EnvironmentalMicrobiology, Institute of Microbiology of the Czech Academy of Sciences, Prague 14200, Czech Republic Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Prague 14200, Czech Republic